RetrogeneDB ID: retro_fcat_425

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:50071614..50072183(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SLC31A1
• Ensembl ID: ENSFCAG00000005512
• Aliases: None
• Description: solute carrier family 31 (copper transporter), member 1 [Source:HGNC Symbol;Acc:11016]

Sequence

>retro_fcat_425
ATGGACCATTCCCACCATAAGGGGACAAGCCATATGGCTGAACAACAGTACAACAGTGCCTTCTCACCACCACCACCTGA
CCACTTCAGCACACTACTCTCATGGTGGGGGAATAGGCAACATGATGATGCCTATGACCTTCTACTTTGGCTTTAAGAAT
GTGGAACTACTGTTTTCTGGTTGGTGGTCAATACAGCTTGAGAAATGGCAGGAGCTTTCTTGGCAGTGTTTTTACTAGCA
ATGTTCTATGAAAGACTCAAGATAGCCTGAGAAAGCCTGCTGCATAAGTCACAAGTCAGCATCTGCTACAATTCCATGCC
TGTACCAGGACCAAAAGGAGACATCCTTATGGGGACACACAGACTGTTGGACAGCAGATGCTGAGCTTTCCTTGTCTCCT
GCAAACAGTGCTGCATGTCATCCACGTGGTCATCAGCTATTTCCTCATGCTTATCTTCATGACCTACAATGGATACCTCT
GCATTGCAGTAGCAGCAGGGGCCGGCACAGGATAACTTCTCTTCAGCTGGAAGAAGGCAATGGTGGTGGACATCATAGAG
CATTGCCAT

Alignment

ORF - retro_fcat_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDHSHHTGTSHMAD-NSTTAPPHHHHHPTTSAHHSHGGGMDGMMMSMTFYFGFKNVELLFSG-LVINTAG
          .DHSHH.GTSHMA..NSTT.P.HHHH..TTSAH.SHGGG...MMM.MTFYFGFKNVELLFSG.LV.NTA.
Retrocopy MDHSHHKGTSHMAE>NSTTVPSHHHHL-TTSAHYSHGGGIGNMMMPMTFYFGFKNVELLFSG<LVVNTA*

Parental  EMAGAFVAVFLLAMFYEGLKIARESLLRKSQVSIRYNSMPVPGPNGTILMETHK-TVGQQMLSFPHLLQT
          EMAGAF.AVFLLAMFYE.LKIA.ESLL.KSQVSI.YNSMPVPGP.G.ILM.TH..TVGQQMLSFP.LLQT
Retrocopy EMAGAFLAVFLLAMFYERLKIA*ESLLHKSQVSICYNSMPVPGPKGDILMGTHR<TVGQQMLSFPCLLQT

Parental  VLHIIQVVISYFLMLIFMTYNGYLCIAVAAGAGTGYFLFSWKKAVVVDITEHCH
          VLH.I.VVISYFLMLIFMTYNGYLCIAVAAGAGTG..LFSWKKA.VVDI.EHCH
Retrocopy VLHVIHVVISYFLMLIFMTYNGYLCIAVAAGAGTG*LLFSWKKAMVVDIIEHCH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	5.62 RPM
SRP017611_kidney	0.00 RPM	13.40 RPM
SRP017611_liver	0.00 RPM	67.02 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_425 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_425 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011908	5 retrocopies	retro_chof_1186, retro_chof_1646, retro_chof_1661, retro_chof_644, retro_chof_776,
Felis catus	ENSFCAG00000005512	1 retrocopy	retro_fcat_425 ,
Macropus eugenii	ENSMEUG00000015425	2 retrocopies	retro_meug_1049, retro_meug_1533,
Microcebus murinus	ENSMICG00000015008	2 retrocopies	retro_mmur_1465, retro_mmur_46,
Myotis lucifugus	ENSMLUG00000015299	1 retrocopy	retro_mluc_2,
Nomascus leucogenys	ENSNLEG00000016636	1 retrocopy	retro_nleu_622,
Pongo abelii	ENSPPYG00000019514	3 retrocopies	retro_pabe_2386, retro_pabe_3548, retro_pabe_847,
Sorex araneus	ENSSARG00000012787	7 retrocopies	retro_sara_101, retro_sara_326, retro_sara_497, retro_sara_584, retro_sara_585, retro_sara_586, retro_sara_730,
Tupaia belangeri	ENSTBEG00000009011	2 retrocopies	retro_tbel_3123, retro_tbel_4170,